Biological Modeling 2020

tree of life

Homepage MSc course Biological Modeling

This page provides practical information about the MSc course Biological Modeling. To learn about the content of this course read the home page. The course Study Guide tells you what material will be covered and needs to be studied, and what exercises to make on the practicals. The course is given on Mondays, Tuesdays and Thursdays, and covers a period of 6-7 weeks, starting in the first (or second) week of September. The first meeting is Monday 31 August 2020 at 13:15h, the first week is a fresh up on math that you can hopefully skip as a MSc student, and the final exam is on Thursday 15 October 2020.

We will work with a number of readers and manuals. They are freely available on the web, the main reader, its answer book, and the math reader (paper copies can be picked up for 20 Euro).

The course starts with a week of mathematics education that be skipped by master students having seen this before. We will cover the material in the math reader, which explains basic concepts in linear algebra: matrices, vectors, eigenvalues and eigenvectors, linearization of ODEs, and the Jacobi matrix (lectures will be recorded and are available for self study). By the end of the first week students know how to determine the stability of equilibrium of a system of non-linear ODEs by linearization and computing a Jacobi matrix. Additionally, we offer a number of basic tutorials to practise the handling of parameter-free equations. We provide self-study tutorials and videos about solving equations, and about sketching functions and isoclines.

Week 2-6 covers the material in the main reader, and has a schedule of lectures in the morning (from 9-11h) and practicals in the afternoon (from 11-15h). During the practicals we will work with R in RStudio, using a R-script called grind.R. Please install RStudio and R on your laptop (see the Introduction to R and the tutorial on installing Grind). The models that we use are provided in this folder.

The seventh week is free to prepare for the exam on Thursday 15 October (good for 5 EC). During this exam you are allowed to use the math reader (and the sheet with formulas). I hope this will be an interesting and challenging course for you!

Note that bachelor students attending this course will continue for 3 more weeks to read papers and do a project.